This application entitled Transcriptome analysis of the adherent-invasive E. coli phenotype is submitted on behalf of Dr. Grace Gathungu in response to PAR-13-074 entitled Small Grants for New Investigators to Promote Diversity in Health Related Research (R03). Dr. Gathungu is an African American new investigator board certified in pediatrics and pediatric gastroenterology. The focus of her research is on biomarkers for diagnosis and treatment of inflammatory bowel disease. This R03 award will provide her with the support necessary to: (1) Conduct a focused research project using microbiology and bioinformatics methodology and develop new research technology (2) Establish an independent academic career in IBD research. To achieve these goals, she is guided by mentors: Ellen Li, MD, PhD who is Professor of Medicine at Stony Brook and has a research focus on intestinal microbiota in IBD, Dr. James Bliska a Microbiologist and expert on Bacteria pathogenesis, & Dr. Wei Zhu a Biostatistician. Additional collaborators are: Dr. John Parkinson, Associate Professor of Biochemistry & Molecular and Medical Genetics at the University of Toronto; Dr. Phillip Tarr, Professor of Pediatrics and Molecular Microbiology at Washington University in St. Louis. Dr. Edgar Boedeker, Professor of Medicine at the University of New Mexico; Dr. Daniel Frank, Assistant Professor in the Department of Medicine at the University of Colorado. There remains a critical need to identify more accurate, reliable and reproducible biomarkers to predict disease progression in patients at risk of serious complications such as fistulae, strictures or surgical management of aggressive Crohn's disease (CD). Evidence from 16S ribosomal RNA gene sequencing reveals that the composition of microbiota in the ileum is altered in patients with ilea CD. There are greater proportions of gram negative bacteria including Escherichia coli. It is hypothesized that Adherent Invasive E coli (AIEC) are associated with increased pathogenic potential in patients with ileal CD. AIEC while predominantly of B2 and D phylotypes are a heterogeneous group of serotypes. Currently no molecular probe can distinguish AIEC from non-invasive bacteria. The main hypothesis is that that highly expressed genes (during infection) can be used to detect AIEC in clinical samples and genes important for bacterial E. coli pathogenesis can be identified by metatranscriptome analysis. Dr. Gathungu proposes to characterize the transcriptional profile of AIEC bacteria during invasion of host mammalian cells. She will identify unique transcripts for AIEC bacteria and also define genes that are differentiall regulated in bacteria. As demonstrated in preliminary studies, she will then examine patient fecal and ileal biopsy samples for genomic probes that are AIEC-specific and can reliably be used in prospective epidemiological studies. Dr. Gathungu will use advanced bioinformatics and molecular biology techniques. In future studies and through R01 funding, Dr. Gathungu will apply this knowledge to prospective studies in pediatric patients with CD.